DUF3487 - PFAM28P - GREMLIN Contacts

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DUF3487 - Protein of unknown function (DUF3487)

PFAM:	PF11990	Sequences: QTIDFLPDRLNREPVVFRGLTASELWLIAGLSAAVGLPLGLLLALLFGSWAMGPTLALLGVALTVFVGGGLLRRLKRGRPDGYLYRRLQLWLARLGLGGSPLITRSGAWSIRRS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	114 (112)
Sequences:	692 (493)
Seq/√Len:	46.6
META:	0.655

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
18_R	70_G	4.410	1.00
13_E	23_S	3.612	1.00
36_G	64_T	3.468	1.00
93_A	104_T	3.057	1.00
94_R	104_T	2.821	1.00
15_V	21_T	2.717	1.00
91_W	95_L	2.716	1.00
82_G	86_R	2.579	1.00
20_L	28_I	2.367	1.00
92_L	97_L	2.359	1.00
87_R	91_W	2.243	1.00
79_R	110_S	2.172	1.00
16_V	28_I	2.063	1.00
76_K	80_P	2.030	0.99
20_L	69_G	1.911	0.99
12_R	81_D	1.885	0.99
51_A	60_G	1.785	0.99
17_F	20_L	1.745	0.98
30_G	34_A	1.643	0.98
11_N	16_V	1.592	0.97
18_R	79_R	1.583	0.97
50_W	53_G	1.494	0.96
50_W	73_R	1.471	0.95
29_A	54_P	1.462	0.95
76_K	109_W	1.387	0.94
19_G	24_E	1.378	0.93
13_E	22_A	1.364	0.93
25_L	65_V	1.338	0.92
105_R	109_W	1.335	0.92
53_G	56_L	1.310	0.91
47_F	56_L	1.238	0.89
85_Y	102_L	1.222	0.88
34_A	38_P	1.221	0.88
54_P	68_G	1.184	0.87
26_W	30_G	1.177	0.86
27_L	87_R	1.176	0.86
30_G	56_L	1.160	0.85
25_L	76_K	1.151	0.85
35_V	39_L	1.145	0.85
68_G	77_R	1.107	0.83
3_I	8_D	1.097	0.82
19_G	28_I	1.097	0.82
32_S	68_G	1.088	0.82
71_L	75_L	1.050	0.79
28_I	49_S	1.032	0.78
11_N	78_G	1.022	0.77
16_V	21_T	1.006	0.76
16_V	64_T	1.006	0.76
17_F	25_L	1.005	0.76
45_L	52_M	1.000	0.76
76_K	81_D	0.995	0.75
17_F	22_A	0.990	0.75
56_L	67_V	0.987	0.75
10_L	15_V	0.981	0.74
72_L	76_K	0.977	0.74
40_G	83_Y	0.954	0.72
41_L	100_S	0.950	0.72
23_S	26_W	0.945	0.72
22_A	25_L	0.937	0.71
30_G	54_P	0.930	0.70
31_L	35_V	0.927	0.70
100_S	114_S	0.919	0.69
68_G	78_G	0.903	0.68
58_L	72_L	0.889	0.67
41_L	95_L	0.877	0.66
10_L	51_A	0.877	0.66
18_R	69_G	0.874	0.65
34_A	48_G	0.869	0.65
54_P	98_G	0.865	0.65
6_L	9_R	0.859	0.64
17_F	76_K	0.858	0.64
69_G	72_L	0.843	0.63
8_D	14_P	0.843	0.63
28_I	31_L	0.838	0.62
89_Q	102_L	0.836	0.62
65_V	75_L	0.830	0.61
35_V	55_T	0.826	0.61
10_L	69_G	0.818	0.60
7_P	20_L	0.818	0.60
30_G	37_L	0.816	0.60
38_P	72_L	0.816	0.60
55_T	98_G	0.812	0.60
55_T	61_V	0.810	0.60
95_L	99_G	0.805	0.59
82_G	102_L	0.792	0.58
103_I	109_W	0.787	0.57
8_D	16_V	0.787	0.57
20_L	65_V	0.782	0.57
40_G	109_W	0.778	0.56
19_G	80_P	0.776	0.56
16_V	88_L	0.775	0.56
14_P	20_L	0.768	0.55
83_Y	86_R	0.767	0.55
37_L	90_L	0.766	0.55
23_S	29_A	0.747	0.53
98_G	102_L	0.744	0.53
7_P	10_L	0.742	0.53
7_P	16_V	0.734	0.52
57_A	70_G	0.733	0.52
50_W	71_L	0.717	0.50
79_R	108_A	0.710	0.50
4_D	39_L	0.708	0.50
61_V	111_I	0.701	0.49
95_L	102_L	0.700	0.49
46_L	110_S	0.698	0.49
10_L	46_L	0.695	0.48
33_A	87_R	0.688	0.48
68_G	102_L	0.684	0.47
69_G	77_R	0.683	0.47
3_I	7_P	0.679	0.47
72_L	89_Q	0.676	0.46
16_V	76_K	0.674	0.46
6_L	10_L	0.669	0.46
13_E	75_L	0.669	0.46
57_A	108_A	0.667	0.45
86_R	89_Q	0.665	0.45
38_P	48_G	0.658	0.45
45_L	51_A	0.655	0.44
54_P	95_L	0.652	0.44
6_L	40_G	0.650	0.44
21_T	69_G	0.647	0.44
71_L	93_A	0.631	0.42
47_F	54_P	0.626	0.42
9_R	76_K	0.621	0.41
71_L	74_R	0.621	0.41
29_A	82_G	0.617	0.41
26_W	65_V	0.614	0.40
39_L	53_G	0.612	0.40
13_E	84_L	0.610	0.40
45_L	53_G	0.608	0.40
18_R	25_L	0.608	0.40
10_L	19_G	0.592	0.38
5_F	20_L	0.588	0.38
44_A	49_S	0.577	0.37
34_A	53_G	0.569	0.36
28_I	35_V	0.566	0.36
67_V	71_L	0.565	0.36
38_P	44_A	0.564	0.36
11_N	77_R	0.561	0.35
54_P	88_L	0.557	0.35
39_L	114_S	0.555	0.35
11_N	14_P	0.550	0.34
40_G	107_G	0.550	0.34
34_A	47_F	0.549	0.34
58_L	62_A	0.547	0.34
13_E	17_F	0.543	0.34
56_L	60_G	0.541	0.34
32_S	107_G	0.538	0.33
36_G	83_Y	0.538	0.33
8_D	13_E	0.536	0.33
9_R	69_G	0.531	0.33
50_W	61_V	0.528	0.32
19_G	69_G	0.525	0.32
3_I	20_L	0.525	0.32
103_I	114_S	0.524	0.32
25_L	74_R	0.522	0.32
32_S	101_P	0.518	0.32
48_G	78_G	0.517	0.32
38_P	101_P	0.517	0.32
97_L	100_S	0.514	0.31
20_L	83_Y	0.510	0.31
47_F	59_L	0.509	0.31
71_L	88_L	0.508	0.31
17_F	53_G	0.508	0.31
36_G	40_G	0.507	0.31
70_G	99_G	0.502	0.30
60_G	64_T	0.502	0.30
48_G	75_L	0.500	0.30

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
2xq2A	2	0.614	21.1	0.908	Contact Map
2zxeA	1	0.7807	17.9	0.91	Contact Map
3ixzA	1	0.7807	11.8	0.918	Contact Map
1q90G	1	0.2632	9.5	0.921	Contact Map
2wswA	3	0.6404	8.7	0.922	Contact Map
2l9uA	2	0.3509	7.2	0.925	Contact Map
3aqpA	1	0.6579	6.9	0.926	Contact Map
1cf2P	4	0.3246	5.7	0.928	Contact Map
2ks1B	1	0.386	4.8	0.931	Contact Map
2cobA	1	0.3947	4.8	0.931	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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